Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants that are considered strongly carcinogenic. A source contribution analysis was conducted by applying positive matrix factorization to measurement data on fine particulate matter in three Japanese cities to identify PAH sources, and a risk assessment was conducted by estimating the toxicity equivalent concentration (TEQ) of each source. Five sources were identified: the major sources of biomass burning, semi-volatile PAHs, and ship and industrial emissions and the minor sources of road traffic and plastic combustion. Biomass burning was a significant PAH source during the cold season. Moreover, biomass burning made a significant contribution to the estimated TEQ for each city. These results suggest that biomass burning is an important source of toxic PAHs. The presented source contribution analysis and risk assessment can help other countries and regions understand the sources and risks of PAHs and collect essential data for control and management.